I've set up dovecot and use it via IMAP. When I'm logged in onto my server is it fine to use dovecot maildir directly with something like Gnus or NotMuch?
I think the definitive answer will have to be "suck it and see" on a test server - the Dovecot Wiki has a section on locking which says
If you can set your client to be read-only (or perhaps mount-rebind the disk read-only) you should be OK.
... or if you can afford the disk space for the mailbox you're working on, you could set up your client to connect to IMAP via localhost and avoid the mess entirely.